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Interlayer functionalization modulation is essential for modifying LDHs and improving their selectivity and adsorption capacity for target pollutants. In this work, Glu@NiFe-LDH was synthesized using a simple one-step hydrothermal method and tested for its ability to remove CrO42− from wastewater. The modification significantly increased the composite material's removal ability by 2–3 times, up to 98.36 mg g−1. The behavior of CrO42− adsorption on Glu@NiFe-LDH was further studied by adjusting the affecting factors (i.e., temperature, pH, contact time, initial concentration, and interfering substance), and the adsorption behavior was confirmed as a spontaneous and chemisorption process. And the result was that Glu@NiFe-LDH demonstrated high capacity, efficiency, stability, and selectivity for the adsorption of CrO42− in a single electrolyte and natural water containing competing anions. Furthermore, molecular dynamics simulations (NVT ensemble) were employed to further reveal the mechanism of glutamic acid modification on LDH at the microscopic scale. Additionally, the IRI analysis method revealed the mechanism of weak interaction between glutamic acid molecules and CrO42−. This study provides a detailed understanding of the intercalation mechanism involved in the amino acid modification of LDHs. It explains the adsorption mechanism of metal oxo-acid radicals by amino acid-modified LDHs from a theoretical perspective. The findings offer experiments and a theoretical basis for designing targeted adsorbents in the future. [ABSTRACT FROM AUTHOR]